|
| Status |
Public on May 04, 2019 |
| Title |
25.2.T12H |
| Sample type |
SRA |
| |
|
| Source name |
Liquid cultures
|
| Organism |
Ostreococcus tauri |
| Characteristics |
strain: RCC745
agent: 25 uM Copper treatment
time point: 12 H incubation
|
| Treatment protocol |
Cultures were incubated with a final Cu concentration of 0.4 µM or 2 µM, for 1, 4 and 12 h after the addition of copper
|
| Growth protocol |
O. tauri RCC745 cultures were grown until the exponential phase (15 x106 cells/mL) in T175 aerated flasks under a 12:12 light-dark cycle (20 µmol photons cm-2 s), in artificial seawater media supplemented with Keller nutrients (0.88 mM nitrate, 22 µM phosphate, and f/2 vitamins)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen cell pellets using the TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA concentrations were determined by absorption at 260 nm, and purity was evaluated by the 260/280 nm absorption ratio. Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
RNAseq libraries were constructed using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) by the NGS Service FASTERIS (Switzerland).
Libraries were multiplexed in one channel of 1 x 50 bp run on a MiSeq run for titration and quality control. Finally, the libraries were sequenced using an Illumina HiSeq 2000 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
25.2.T12H
HDB-17
|
| Data processing |
Raw image data were converted into sequence data by base-calling, defined as raw reads.
Pandaseq was used to assemble the paired-end sequences with default values.
All sequences were searched for homologies against the KEGG database and against the most recent O. tauri genome annotation using the DIAMOND protein aligner.
The DEseq2 routine was applied for comparisons between treatments
Genes with absolute Log2FC values over 0.3 and p-adjusted values below 0.1 were selected for further analysis.
Genome_build: Ostreococcus tauri reference genome was used for sequence alignment (Blanc-Mathieu et al., 2014).
Supplementary_files_format_and_content: Excel file with log2fold change of gene expresion and the associated statistical values.
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
May 04, 2018 |
| Last update date |
May 04, 2019 |
| Contact name |
Rodrigo De la Iglesia |
| E-mail(s) |
[email protected]
|
| Organization name |
Pontificia Universidad Católica de Chile
|
| Street address |
Portugal 49
|
| City |
Santiago |
| ZIP/Postal code |
8330025 |
| Country |
Chile |
| |
|
| Platform ID |
GPL24963 |
| Series (1) |
| GSE114058 |
Transcriptional response of Ostreococcus tauri to Cu challenge |
|
| Relations |
| BioSample |
SAMN09072897 |
| SRA |
SRX4042700 |
